I suggest that you may be trying to pack too much information or too many thoughts into one sentence, especially if these parentheses are long, as you say. If you are trying to qualify a particular part of the sentence, try removing the parenthetical thought and use it to construct a whole following sentence that qualifies, explains, or elaborates on the first. Think of the parenthetical thoughts as knots on a string that need untying into sentences of their own.
This should help the reader grasp your ideas more easily. It could also improve the flow of your writing by eliminating the stop-and-go reading and parsing caused by too many parenthetical, distracting expressions.